With provinces no longer using PCR testing for most cases, testing wastewater for SARS-CoV-2 has become an increasingly important form of COVID surveillance

John Giesy helps run a level two biosafety lab at the University of Saskatchewan. “Level four would be where you’re working with things like anthrax, and everyone is in hazmat suits,” the toxicologist and environmental chemist explains.

At the Saskatoon biolab, people sit before fume hoods, “where we vent things and filter things, so we’re not releasing anything to the environment, and our people aren’t exposed.”

One of the things they’re filtering is wastewater, searching for signals of SARS-CoV-2 from human stool.

Sewage samples are collected over a 24-hour period at the city’s wastewater treatment plant. An automatic sampler takes little sips every hour. One of Giesy’s people goes down to the plant three times a week, grabs the sample and brings it back to the lab. All the testing is done inside those special hoods, so there’s really no exposure, really no smell. “It’s very dilute,” Giesy said. You don’t see much. “There are some particulates in there. But it’s grey water and black water, mixed together. So, it’s not all that disgusting.”

Saskatoon is a city of about 300,000. If five people are infected with COVID, Giesy will see it in the wastewater. “It’s pretty sensitive.”

With PCR testing largely “going the way of the dodo,” as infectious diseases doctor Andrew Morris recently wrote is his newsletter, and with no reporting or tracking of home-based rapid test results, measuring the number of virus particles in sewage has become an increasingly important form of COVID surveillance. “Earlier in the pandemic, there were folks like me who said, ‘Oh my God, it’s going to be so valuable,’” said Doug Manuel, who leads the wastewater group for a national network in Canada tracking COVID-19 variants. Others weren’t nearly so convinced, until the case reporting system collapsed.

Even people without symptoms of COVID shed virus in their poop. A wastewater viral signal increases two to seven days before confirmed case numbers start to rise. Quebec City once hired more contact tracers when the wastewater gave out smoke signals of an imminent outbreak. Yellowknife dodged community-wide transmission in December 2020, when wastewater picked up undetected cases of COVID. All recent travellers were urged to get tested. Five cases showed up in people who were at the end of their self-isolation period.

SARS-CoV-2 has been detected in the outflow of university dorms, nursing homes and prisons. Sewage testing, American epidemiologist and public health scientists Eric Feigl-Ding told Salon this month, is the most “objective, unbiased, politics-free kind of testing.” It’s not meant to replace diagnostic testing, but it monitors the whole community; it doesn’t rely on people being symptomatic or people willing to be tested, and it can help detect emerging variants sooner. It’s also poised to expand in our post-pandemic world, because sewage can give surprisingly detailed information about the health and habits of the people contributing to it.

Wastewater-based epidemiology, as the field is known, can be used to mine sewage samples for influenza, heroin, cocaine, methamphetamine and other illicit drug use, antibiotic-resistant super bugs and metabolic diseases like obesity. Obese people have clear differences in their gut microbiome. In one study, researchers who scoured untreated sewage samples collected from 71 American cities for specific species of gut bacteria were able to predict whether the population was lean or obese, with 81 to 89 per cent accuracy.

Once infected with COVID, people typically begin shedding the virus in their stool several days before they start coughing, feeling feverish or showing other symptoms, and they can keep shedding for up to 45 days. It doesn’t depend on disease severity, and kids and adults are equally likely to excrete SARS-CoV-2 RNA in their feces, a brief from Ontario’s COVID-19 science table reported.

Canada was one of the first out the gates for wastewater surveillance for SARS-CoV-2. It hasn’t been all smooth sailing. At first, university-based labs took the initiative. “We went in and started talking amongst each other and developing methods and sampling,” said Manuel, a public health doctor and senior scientist with the Ottawa Hospital Research Institute. “Really, the academic labs carried it forward whatever way they could with whatever money they could.”

In Quebec, a pilot project led by McGill University civil engineering professor Dominic Frigon began testing wastewater for SARS-CoV-2 in 2020. The province scrapped the testing when the funding came to an end in December, just as Omicron was firing up. “Early in this Omicron wave we were wondering, ‘Are we passed the peak? Are we at the peak? Where’s the peak?’” Frigon said in an interview with the Montreal Gazette. After political pushback, the province announced plans in March to resume wastewater testing for COVID in four cities — Montreal, Laval, Gatineau and Quebec City. Federal Health Minister Jean-Yves Duclos toured Frigon’s lab this week, later praising the team’s “life saving work” in a tweet.

“Wastewater sampling is a leading indicator — a harbinger of sorts,” said Dr. David Naylor, co-lead of Canada’s COVID-19 immunity task force. Hospitalizations lag any wave of infections by at least a few days. In the U.S., Omicron-associated mutations were picked up in wastewater sampling in California, Texas and New York State at least a week before the first American case was identified on Dec. 1.

Wastewater sampling is a leading indicator — a harbinger of sorts

As with everything, there are pros and cons, Giesy said. The pros: It’s relatively fast, and relatively inexpensive — about one-one hundredth the cost to get the same amount of data by testing everyone with PCR, one of Giesy’s colleagues estimates — and an entire city can be sampled at once. Most people, if infected with COVID, excrete the virus, whether they have symptoms or not. Testing sewage provides a measure of the amount of virus circulating. Is there an increase, a rapid increase? Are things stabilizing?

The cons: Viral RNA breaks down in wastewater pretty quickly. It’s not terribly stable. The transit time between flushing and “sample collection point” can affect how much RNA remains intact, meaning having to work with degraded material. Meltwater in the spring, or huge downpours draining into sewers can muddy things by diluting samples. The early warning, “heads up” window changes with each new variant. With Delta, “we could give about two weeks’ notice between when we would see a signal coming up real fast in wastewater before people ended up in hospital,” said Giesy, whose team monitors wastewater from Saskatoon, Prince Albert and North Battleford. With Omicron, it’s six days. Omicron’s incubation time is shorter, its transmission is higher, and people are getting sicker sooner, though not as sick as they did with Delta.

Despite its relative newness for COVID (sewage testing has been used for decades to monitor for diseases like polio) wastewater testing has influenced public health decisions and interventions in Ontario and elsewhere. Early in the pandemic, “we said things are ramping up in Saskatoon, so they moved a lot of people and vaccine up here early on,” Giesy said.

“Things cruised along for a while and when we stopped testing and the data weren’t really flowing in, the province contacted me and said, ‘We’re going to have to rely on your data. How do we do that?’ So now we have a working group. We provide them with data weekly, and they use it in models to predict what’s happening.” The scientists try to be as accurate as they can. It isn’t real-time data. It takes time to process. Giesy’s team spends all of Fridays and Saturdays working up that week’s three samples. By the time he gets the data on Saturday, the first sample is nearly a week old. He shares his data with the public, spending Monday mornings juggling media calls.

Wastewater testing for SARS-CoV-2 is currently performed at about 250 sites across Canada, but, of those sites, only 25 municipalities have publicly viewable data, and only a fraction make the data easily available, which frustrates Manuel. When he asks, why not be more open, people — public health, other academics — tell him the science isn’t ready, that we don’t understand it enough, that the data are hard to interpret. “People do have a tendency of interpreting small changes, and daily changes”, he said, which may be one reason why data isn’t more widely published. Twitter is full of, “it looks like WW is plateauing!” and the signal continues to climb a few days later. But the major calls, Manuel said, “have been amazing.” When Ontario announced in January it was gradually easing restrictions, hospitalizations were still going up, but the sewage signal was going down. “For the first time in a pandemic wave Ontario opened up when hospitalization or cases were still climbing,” Manuel said. “Wastewater was influential in that decision.”

Surveillance is also done by the National Microbiology Lab in Winnipeg. But while many countries have a national scheme, ‘we don’t

have anything we could call a coordinated national program,” Manuel said. In Ontario, about 70 to 80 per cent of the population is covered by wastewater testing. In the Netherlands, samples of untreated sewage are taken four times a week at more than 300 sewage treatment plants, meaning the sewage of virtually every Dutch household, more than 17 million people, is tested for SARS-CoV-2.

Sewage surveillance uses the same PCR testing method used to test for the virus in nose swabs, with a few added steps. It provides a reading of the amount of virus circulating in the community, but at all stages of disease. Recovered people can still be shedding, so there’s a chance of picking up old infections as well. Flow rates can also be problematic. It can take 72 hours for poo flushed down a toilet in Ottawa’s west end before it ends up in the city’s treatment facility. In cities like Hamilton, industrial effluent may affect samples. “Last spring in Ottawa we had this big melt event and it made it very difficult to interpret the signal,” Manuel said. A two-fold difference from one day to another isn’t uncommon. “You can have a 10-fold difference in what is measured in wastewater, and not because there’s a 10-fold difference in the level of virus in the community but because of how it’s sampled and how it’s going through the system.” And while wastewater levels correlate closely with how much disease is out there, it’s the total population that’s being sampled. We don’t know what age group, or who, specifically?

For these reasons and more, wastewater surveillance isn’t meant to replace human testing.  “I think it’s important to recognize what it is and not make it something that it isn’t,” Manuel said. What it is, he said, is a highly useful piece of information that complements other forms of information, like hospitalizations. No single indicator tells the entire story, Frigon said. Sewage sampling “is not a panacea.” Plus, there are field challenges. “It’s not the kind of thing you could just turn over to anyone to run,” Giesy said. There’s also a risk of stigmatizing communities. “We do five First Nations. Our deal with the First Nations is, we collect the data weekly, we give it to them and it’s really up to them to do whatever they want with it. We don’t release that publicly. We don’t want to stigmatize communities.” The work is funded by the Public Health Agency of Canada, which is looking at where to go next with wastewater surveillance. “We can look at other viruses, we can do all kinds of monitoring,” Giesy said.

When they know what they’re looking for, they use PCR. When searching for new and emerging variants, they use genetic sequencing, looking for mutations in genome fragments. It’s harder than testing a single human because there can be many variants in soupy sewage sludge. Still, “If you try to imagine an early detection system for variants, the list is pretty short,” Manuel said. “I don’t know what you would have that is potentially feasible for world coverage other than wastewater.” You can test anywhere, he said — open sewage systems, wastewater lagoons. Variants have come from Peru, Columbia and South Africa. Manuel’s lab is working with the World Bank and the Rockefeller Foundation. “People see the potential for middle- and low-income countries,” he said, but new variants can emerge anywhere there are high levels of infection. In Haiti, after a devastating earthquake killed more than 100,000 people in 2010, personal seismometers were distributed to the homes of volunteers, and a “citizen seismic network” set up to help capture the location and magnitude of earthquakes, and monitor for dangerous aftershocks. Frigon wonders if a similar type of participatory science could be used with wastewater surveillance, by having people sampling neighborhood sewers. “We don’t know exactly where this water is coming from.”

Meanwhile, the wastewater sleuths are monitoring for Omicron and its subvariants BA.1, 2, 3, and now the X variants, which are recombinants, or combinations of different variants. No one knows what COVID plot twist could come next. Nationally, Omicron is peaking. “Globally, deaths are plummeting. It seems likely that the pandemic is waning,” said University of Ottawa epidemiologist Raywat Deonandan. The sixth wave may be quashed by the beginning of the summer.

“The big question is whether the hard-won population immunity garnered by vaccination and mass infection is temporary,” Deonandan said. Immunity from antibodies is waning. But cellular immunity, or memory immunity, might linger, “so that any existential threat to our health-care system is no longer present.”

Still, COVID always surprises. “Maybe five years from now we’ll have more information and be given guidance that a more deadly virus is less likely,” Manuel said. “But we’re not at that point today.”

Everyone is trying to read the tea leaves, it seems.

Manuel will keep reading the water.

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